SMTL ID : 2vqj.1

Structure of HDAC4 catalytic domain bound to a trifluoromethylketone inhbitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.1: 4 residues within 4Å: Chain A: T.16, L.19, K.20, F.102 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.194, D.196, H.198, S.217, L.218, H.219 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.194, A:D.196, A:H.198, A:S.217, A:L.218 K.3: 4 residues within 4Å: Chain A: F.207, D.210, V.213, F.244 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.207, A:D.210, A:V.213, A:F.244, H2O.6

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: G.36, R.37, I.38, R.154 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.37, A:I.38 Water bridges: A:Q.39 Salt bridges: A:R.37, A:R.154 SO4.5: 4 residues within 4Å: Chain A: D.255, P.256, N.366, A.367 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.367 Water bridges: A:N.368 SO4.6: 2 residues within 4Å: Chain A: S.72, E.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.73

1 x TFG: 2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHEN-2-YL}ETHANE-1,1-DIOL

TFG.7: 13 residues within 4Å: Chain A: P.156, H.158, H.159, G.167, F.168, C.169, D.196, H.198, F.227, D.290, E.329, G.330 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.168, A:F.168, A:F.227 pi-Stacking: A:H.198

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: D.196, H.198, D.290 Ligands: TFG.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.196, A:D.196, A:H.198, A:D.290 ZN.9: 4 residues within 4Å: Chain A: H.21, C.23, H.34, C.107 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.21, A:C.23, A:H.34, A:C.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bottomley, M.J. et al., Structural and Functional Analysis of the Human Hdac4 Catalytic Domain Reveals a Regulatory Zinc-Binding Domain. J.Biol.Chem. (2008)

Release Date

2008-07-08

Peptides

HISTONE DEACETYLASE 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HISTONE DEACETYLASE 4

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